Variant report

Variant	rs10399840
Chromosome Location	chr1:184433511-184433512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184353853..184357203-chr1:184430668..184434777,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction
ENSG00000271387	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10489724	0.92[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10489725	0.92[ASW][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10489726	0.92[ASW][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10489728	1.00[JPT][hapmap]
rs12067483	0.96[AFR][1000 genomes]
rs12079052	1.00[JPT][hapmap]
rs12084533	1.00[JPT][hapmap]
rs12737779	0.96[AFR][1000 genomes]
rs13374607	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13375073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535133	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1547606	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823210	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651207	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68189478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10399840	NPL	cis	parietal	SCAN
rs10399840	EDEM3	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184419200-184438400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:184424000-184436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:184425400-184442200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:184427400-184443800	Weak transcription	Esophagus	oesophagus
5	chr1:184427400-184444000	Weak transcription	Lung	lung
6	chr1:184427400-184448400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:184429000-184454800	Weak transcription	Aorta	Aorta
8	chr1:184429400-184434800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:184429400-184449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:184429600-184434600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:184429600-184442200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:184429800-184436600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:184430400-184439000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:184430600-184433800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:184430600-184434600	Weak transcription	Right Atrium	heart
16	chr1:184430600-184436400	Weak transcription	Pancreas	Pancrea
17	chr1:184430600-184444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:184430600-184449800	Weak transcription	Right Ventricle	heart
19	chr1:184430600-184450000	Weak transcription	Fetal Stomach	stomach
20	chr1:184430800-184434800	Weak transcription	Left Ventricle	heart
21	chr1:184431000-184436400	Weak transcription	Ovary	ovary
22	chr1:184431400-184446400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:184431600-184434200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:184431600-184434800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:184431600-184435000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:184431600-184435400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:184431600-184436600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:184431800-184434800	Weak transcription	Fetal Heart	heart
29	chr1:184431800-184440600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:184431800-184447600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:184432000-184433800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:184432000-184433800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:184432000-184443400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:184432600-184433600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:184432600-184433600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:184432600-184433800	Enhancers	NHEK	skin
37	chr1:184432800-184433600	Enhancers	HMEC	breast
38	chr1:184432800-184434200	Enhancers	Psoas Muscle	Psoas
39	chr1:184433000-184435000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:184433200-184434800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:184433200-184442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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